From 3634942b4f7ef973c25786a03748e8e8b6f4b40b Mon Sep 17 00:00:00 2001 From: Tazro Inutano Ohta Date: Thu, 29 Aug 2024 17:16:57 +0900 Subject: [PATCH] Initial commit --- LICENSE | 121 ++++++++++++++++++++++++++++++++++++ README.md | 84 +++++++++++++++++++++++++ paper/biohackrxiv.png | Bin 0 -> 6858 bytes paper/paper.bib | 20 ++++++ paper/paper.md | 114 +++++++++++++++++++++++++++++++++ paper/use-this-template.png | Bin 0 -> 16878 bytes 6 files changed, 339 insertions(+) create mode 100644 LICENSE create mode 100644 README.md create mode 100644 paper/biohackrxiv.png create mode 100644 paper/paper.bib create mode 100644 paper/paper.md create mode 100644 paper/use-this-template.png diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..0e259d4 --- /dev/null +++ b/LICENSE @@ -0,0 +1,121 @@ +Creative Commons Legal Code + +CC0 1.0 Universal + + CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE + LEGAL SERVICES. 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Affirmer understands and acknowledges that Creative Commons is not a + party to this document and has no duty or obligation with respect to + this CC0 or use of the Work. diff --git a/README.md b/README.md new file mode 100644 index 0000000..e729e15 --- /dev/null +++ b/README.md @@ -0,0 +1,84 @@ +# BioHackrXiv Publication Template + +Minimal example of a [BioHackrXiv](https://biohackrxiv.org/) publication that can be generated with the +[Preview Service](http://preview.biohackrxiv.org/). + +## Step 1: Clone this Template Repository + +This repository is a template repository. This means that you can hit the green "Use this template" +button (after logging in) to use it as a template to start a new BioHackrXiv Publication: + +![Screenshot of the green "Use this template" button.](paper/use-this-template.png) + +## Step 2: Configuring the Markdown + +The publication Markdown is found in the `paper/paper.md` file. At the top you can edit the +YAML code with metadata. It is important to get this part correct, because otherwise the PDF +generation will fail. The metadata looks like this: + +```yaml +title: 'BioHackEU22 Report for Project 26: Shedding the light on unknown chemical substances' +title_short: 'BioHackEU22 #26: unknown chemical substances' +tags: + - cheminformatics + - PubChem + - unknown chemical substances +authors: + - name: Egon Willighagen + affiliation: 1 +affiliations: + - name: Dept of Bioinformatics - BiGCaT, NUTRIM, FHML, Maastricht University, Maastricht, NL + index: 1 +date: 7 November 2022 +cito-bibliography: paper.bib +event: BH22EU +biohackathon_name: "BioHackathon Europe 2022" +biohackathon_url: "https://biohackathon-europe.org/" +biohackathon_location: "Paris, France, 2022" +group: Unknown chemical substances group +# URL to project git repo --- should contain the actual paper.md: +git_url: https://github.com/biohackrxiv/publication-template +# This is the short authors description that is used at the +# bottom of the generated paper (typically the first two authors): +authors_short: Egon Willighagen \emph{et al.} +``` + +### Which metadata to update? + +#### To change + +The following fields should be changed: + +* title +* title_short +* tags +* authors +* affiliations +* date +* group +* authors_short + +Particularly important to update is the following field, which should point to +your clone of the template, instead of the template itself: + +* git_url: https://github.com/biohackrxiv/publication-template + +#### Only update for other BioHackathons + +The following fields should only be changed if you are not writing for the BioHackathon Europe 2022: + +* event: BH22EU +* biohackathon_name: "BioHackathon Europe 2022" +* biohackathon_url: "https://biohackathon-europe.org/" +* biohackathon_location: "Paris, France, 2022" + +## Step 3: Writing the article + +A full Markdown example is given in [paper/paper.md](paper/paper.md). This includes instructions how to include +figures, tables, and annotate citations with the Citation Typing Ontology. + +## Step 4: Previewing the paper as PDF + +This repository can be converted into a preview PDF with BioHackrXiv [Preview Server](http://preview.biohackrxiv.org/). +The preview website asks for the link to your repository and will automatically find the `paper.md` and create an PDF. + diff --git a/paper/biohackrxiv.png b/paper/biohackrxiv.png new file mode 100644 index 0000000000000000000000000000000000000000..9aaff078f42aa19fc0eb05e4caa67d2d8f835c7f GIT binary patch literal 6858 zcmV;*8a3sKP)RCt{2UF~(Ny3)>m*ZmK-0&^;WU4hvZ*r~uy1!h-Zrvf__ z*r_0-0^S8MzAba9uZ8VhEEeeY@xTER5@Ulgo6Rnl3wnlo zI3ACa$pp1;v?Sc`_e6Ui9v;RqtU}mMLSk&NUdrHk-g>=uS7EzcF4O50HEXmaJfF`u z+dFPyXfFwgv6)OJY!(vpbuyVaXDF6sxmvAIQv?_X39-3b!}C0#ijUY5wvmK4#|GR_ zXl~Q#)Rp!VD>T`m_e zg6J0KF)#`HlU?2AYJVVHzOpSAr%6a#3c~jC7`-qYl7t<{Mg@e0xmvAct8afe9*=~S zCaC2o2?=vo-Dh?_pFu~VTinJlB-AoCifHONGftOkD*tC8nnO3Z88$&oFTf2Pi zC!x^d)oXPFonka0-6lvV9G=x`g>Ezr!avmU^?*Z`8gu-=~AIPDS;_;rl;=s5|LP9rDG+xZ4|KXijbc+&*;NCxugbYOdp@CcnA%K1r zhN0*#2p366Sm}*OXe<}LV@NkK*$ju{*hNAHVsUDed7uSYDOFk8-6A0!)ZUbY#)RS9 z+Z+EY>c#@0cA00Or6eTObOyso@gQVTMHo6nLRr)vo7P~mqHl`<-d0h4Xn__X-7<4` zC9BxxnhynuNx3;Z=m8in%*rW{(3TWFWLAGkwPo_RT#*y_~^Da%(pgt>@#smewTv z`uYM(XHUDn^v)zv&JSR~B5ux*koF&hVMw#0JHSuV8&kSSNH5_{-Bd(%580!-kkCx} z9}%WQEZp`m&@mD+$W$rM^LmZ20iJhyN_8ip`Vx-C7e?zkS6xVGEEgUNL&Ai?7`%|F zdn9BK8rgmGkRMli`>P`fZ+h@>!(}sxaL23Ep6EzIGr~|-KSc$yelrPINhq6Mz48!< zCPMzSCLytev-JE%C0hyePjQ>4BMAvzQ7`aJ01#?VmK5`Ln1l@5?H2TGfA%5R9VV#N zf`l?PTPWxVYllVKVqXqF1nTQlM-t*E^b~<8a~3fA35)&NQ%>J`5@MaFQSd|~fKXCm z6dRF{a5xbrpSsalqeYHbcM|q33~!pd=kwWS29AV;LLT;1-yYBdef~GpNl3^vm5Qvi z`;?#h#M=_+PC~3JY8)Co?sa?Fuh`GP@sJRYbWgrG{`thTRv{s=gf|UBAe7IJ>0nw& z*i%TijDfYe>jVQwMMAtg+{bTeAt4=(*IH0uHw<>ww0LHB65=JYI}?NqmgdItt4H-E=$()zQgh(zkJ9xjKqfN|lgqp%%K`Ze=mFVHkoq zwfs3{0F-iJ@0iq8g2^*#VVaSq+a4fYDLP^NbYe^3KB_Vz$ z;hn-VkO0_aHCB1CJ4Q=FuvekJb1idovxg|=9}pyD=;@?>CrGFm(yh)wSy=!xl^45X zwCX5xlh%J@)diy{ia3sc{rdI!`3XK`=3JiVQ52!?wZZ%Q``|}V4F%u#d1FE7I1y^0 z7;Kl7`AE@+?wsFbfapU>LiN4%n`uE!Gk}03-0%0YEe*X#P&pw9Z|aIFGEgzd)=cHa zju^8f6t0dKhr=NVf|r*U^vOTycz|gT1ZkQI72VIz&&S8dIF9o?N8cMQf*{~^#m~>r z+SjEb1KBRC%At{F&JXSi14JK65`q(g@WM%yiU`9HXC$CskU|!~O}KopYoP^Pk%Tf~ zcvA+pI55vl<;5--vm^w&;k@-#6vcc#|Mlw^wiRnPH`vuUolaVeiX=&jq7bGsy}Y~x zK`@4+XB7|x0k5Keetyp9b3z6(y*bJ5z1Hco-{l-S+Etl^O$Z{D@a`XTbF=M1^zFY91OYHAw0qcm-`{LD!epGPs-B;pqbRaE>Z${T?P6wm zmSx1aGy>R}w9Ya#Ky(|z)-cpvk$4@wDGa+5|CLE>6~~}kl2GWK>Zxq3u`?E<(}5XW&*6vAzc)9Li{=g%ZbWKDJp%jNR*^%cMJ z$Hzw>4fK7VpAuD7^*4x(VSwn`B_S_onAOCKCZZH)>+lq?j^2z0)^Z?>P*BjpBCbe6 zS<@JLI_pljGid{yB%#oa;d$P4I+f{i-QC<^-q4z%uA|X}Rl^vB+Zaxe5Hk>jMi@J? 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I.}, + title={{DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases}}, + journal={Bioinformatics}, + year={2016}, + volume={32}, + number={14}, + pages={2236--2238}, + doi={10.1093/bioinformatics/btw214}, +} + +@article{CiTO, +author = {Shotton, David}, +journal = {Journal of Biomedical Semantics}, +number = {Suppl 1}, +year = {2010}, +pages = {S6}, +title = {CiTO, the {Citation} {Typing} {Ontology}}, +volume = {1 Suppl 1}, +} diff --git a/paper/paper.md b/paper/paper.md new file mode 100644 index 0000000..fa96766 --- /dev/null +++ b/paper/paper.md @@ -0,0 +1,114 @@ +--- +title: 'BioHackEU23 report: Template for the very long title' +title_short: 'BioHackEU23 #26: unknown chemical substances' +tags: + - cheminformatics + - PubChem + - unknown chemical substances +authors: + - name: First Author + affiliation: 1 + - name: Last Author + orcid: 0000-0000-0000-0000 + affiliation: 2 +affiliations: + - name: First Affiliation + index: 1 + - name: Second Affiliation + index: 2 +date: 8 November 2023 +cito-bibliography: paper.bib +event: BH23EU +biohackathon_name: "BioHackathon Europe 2023" +biohackathon_url: "https://biohackathon-europe.org/" +biohackathon_location: "Barcelona, Spain, 2023" +group: Project 26 +# URL to project git repo --- should contain the actual paper.md: +git_url: https://github.com/biohackrxiv/publication-template +# This is the short authors description that is used at the +# bottom of the generated paper (typically the first two authors): +authors_short: First Author \emph{et al.} +--- + + +# Introduction + +As part of the BioHackathon Europe 2023, we here report... + +# Formatting + +This document use Markdown and you can look at [this tutorial](https://www.markdowntutorial.com/). + +## Subsection level 2 + +Please keep sections to a maximum of only two levels. + +## Tables and figures + +Tables can be added in the following way, though alternatives are possible: + +Table: Note that table caption is automatically numbered and should be +given before the table itself. + +| Header 1 | Header 2 | +| -------- | -------- | +| item 1 | item 2 | +| item 3 | item 4 | + +A figure is added with: + +![Caption for BioHackrXiv logo figure](./biohackrxiv.png) + +# Other main section on your manuscript level 1 + +Lists can be added with: + +1. Item 1 +2. Item 2 + +# Citation Typing Ontology annotation + +You can use [CiTO](http://purl.org/spar/cito/2018-02-12) annotations, as explained in [this BioHackathon Europe 2021 write up](https://raw.githubusercontent.com/biohackrxiv/bhxiv-metadata/main/doc/elixir_biohackathon2021/paper.md) and [this CiTO Pilot](https://www.biomedcentral.com/collections/cito). +Using this template, you can cite an article and indicate _why_ you cite that article, for instance DisGeNET-RDF [@citesAsAuthority:Queralt2016]. + +The syntax in Markdown is as follows: a single intention annotation looks like +`[@usesMethodIn:Krewinkel2017]`; two or more intentions are separated +with colons, like `[@extends:discusses:Nielsen2017Scholia]`. When you cite two +different articles, you use this syntax: `[@citesAsDataSource:Ammar2022ETL; @citesAsDataSource:Arend2022BioHackEU22]`. + +Possible CiTO typing annotation include: + +* citesAsDataSource: when you point the reader to a source of data which may explain a claim +* usesDataFrom: when you reuse somehow (and elaborate on) the data in the cited entity +* usesMethodIn +* citesAsAuthority +* citesAsEvidence +* citesAsPotentialSolution +* citesAsRecommendedReading +* citesAsRelated +* citesAsSourceDocument +* citesForInformation +* confirms +* documents +* providesDataFor +* obtainsSupportFrom +* discusses +* extends +* agreesWith +* disagreesWith +* updates +* citation: generic citation + + +# Results + + +# Discussion + +... + +## Acknowledgements + +... + +## References diff --git a/paper/use-this-template.png b/paper/use-this-template.png new file mode 100644 index 0000000000000000000000000000000000000000..2d67fe60b29f4da9e7e5a04b685f716058129298 GIT binary patch literal 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